BACKGROUND The aim of this work was to compare autonomic nervous system activity between eyes with axial and non-axial myopia and to investigate the relationship between autonomic nervous system activity and axial length (AL) in children. MATERIAL AND METHODS Seventy-eight eyes of 78 children were included in this study. Static and dynamic pupillary responses, including pupil diameter, latency, and velocity of pupil contraction and dilation, were recorded using automatic pupillometry to evaluate autonomic nervous system activity. AL was measured using the IOL-Master device. RESULTS In terms of static pupillary responses, the pupil diameter at mesopic condition (1 candelas/m²) (PD1) (4.06±0.64 vs 3.80±0.87 mm, P=0.045) and pupil diameter at low photopic condition (10 candelas/m²) (PD10) (3.40±0.49 vs 3.22±0.66 mm, P=0.046) were significantly larger in axial myopic eyes than in non-axial myopic eyes. In terms of dynamic pupillary responses, velocity of pupil contraction (Vel-C) (5.93±0.89 vs 6.75±1.60 mm/s, P=0.019) and velocity of pupil dilation (Vel-D) (2.28±0.38 vs 2.89±1.17 mm/s, P=0.002) were significantly slower in axial myopic eyes than in non-axial myopic eyes. Moreover, PD1 and PD10 were significantly and positively associated with AL, while Vel-C and Vel-D were significantly and negatively associated with AL (all P<0.05). CONCLUSIONS There was significant decrease in autonomic nervous system activity in axial myopia compared with non-axial myopia, and autonomic nervous system activity was significantly and negatively associated with AL in children. Decreases in autonomic nervous system activity in axial myopia may contribute to the excessive axial elongation in pediatric axial myopia.